This small business innovation research phase I project builds on IonSpec's success in developing affordable, high quality Fourier transform mass spectrometry (FTMS) instrumentation and on their 15 years of expertise in the FTMS field. The research will develop the next generation of analysis tools for FTMS data that will allow an order of magnitude improvement in the accuracy of mass measurements. Currently Fourier transform mass spectrometry provides the highest routinely available mass accuracy. This is limited to 1 ppm by the uncertainty principle of the Fourier transform and frequency drift caused by the coulombic repulsion among the ions. Recently a new method for analyzing time domain data of this type has been developed called the Filter Diagonalization Method. This method is not affected by the uncertainty principle and has been used to correct frequency drifts in nuclear magnetic resonance experiments. The objective of this Phase I research project is to develop the Filter Diagonalization Method for broad band FTMS data, incorporate these algorithms into the IonSpec Omega data acquisition and analysis package, demonstrate the improvement in mass accuracy on protein tryptic digests, and use this improvement in mass accuracy for enhancement of protein database searches and elemental composition calculations. PROPOSED COMMERCIAL APPLICATION: NOT AVAILABLE